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S13-like H2TH domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   S13-like H2TH domain [ 81297]
Superfamily:   S13-like H2TH domain [ 46946] (3)
Families:   Ribosomal protein S13 [ 46947]
  Middle domain of MutM-like DNA repair proteins [ 81626] (3)
  Topoisomerase VI-B subunit middle domain [ 81705]


Superfamily statistics
Genomes (3,252) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 7,775 43,187 25
Proteins 7,770 43,157 25


Functional annotation
General category Information
Detailed category Translation

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular nitrogen compound metabolic process 0.000000000000148 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.000000001071 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0000009429 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0001296 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0001572 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0003419 Least Informative Direct
Biological Process (BP) response to stimulus 0.005447 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.7881 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular response to stress 0.000000000001137 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0.000001237 Moderately Informative Direct
Biological Process (BP) peptide metabolic process 0.000001544 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.1945 Moderately Informative Inherited
Biological Process (BP) gene expression 0.5382 Moderately Informative Inherited
Biological Process (BP) cellular response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) DNA metabolic process 0.000000001915 Informative Direct
Molecular Function (MF) hydrolase activity 0.0000008871 Least Informative Direct
Molecular Function (MF) binding 0.3541 Least Informative Inherited
Molecular Function (MF) structural molecule activity 0.0000001247 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.0000001957 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.0002583 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on glycosyl bonds 8.27e-16 Informative Direct
Molecular Function (MF) hydrolase activity, hydrolyzing N-glycosyl compounds 0 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.006763 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.001216 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.181 Least Informative Inherited
Cellular Component (CC) ribosome 0.0000000000001875 Moderately Informative Direct
Cellular Component (CC) cytosolic part 0.000000005117 Moderately Informative Direct
Cellular Component (CC) small ribosomal subunit 0 Informative Direct
Cellular Component (CC) cytosolic ribosome 0.01139 Informative Inherited
Cellular Component (CC) cytosolic small ribosomal subunit 0.00001678 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Isomerases1Least InformativeInherited
Enzyme Commission (EC)Hydrolyzing N-glycosyl compounds0InformativeDirect
Enzyme Commission (EC)Other carbon-oxygen lyases0InformativeDirect
Enzyme Commission (EC)Sole sub-subclass for isomerases that do not belon1InformativeInherited
Enzyme Commission (EC)DNA-formamidopyrimidine glycosylase0Highly InformativeDirect
Enzyme Commission (EC)DNA-(apurinic or apyrimidinic site) lyase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processDNA repair0InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationIsomerase1Moderately InformativeInherited
Post-translational modificationGlycosidase0InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect
Post-translational modificationrRNA-binding0InformativeDirect
Post-translational modificationtRNA-binding0Highly InformativeDirect
Post-translational modificationTopoisomerase0.0000000000244Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010979 SSF46946 Protein matches
Abstract

Ribosomal protein S13 is one of the proteins from the small ribosomal subunit [PubMed12464183]. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. S13 contains thee helices and a beta-hairpin in the core of the protein, which form a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension.

This H2TH motif can be found in other proteins as well. In the DNA repair protein, MutM (formamidopyrimidine DNA glycosylase; Fpg), the middle domain contains the H2TH motif. MutM is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidatively damaged bases (N-glycosylase activity) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity) [PubMed10921868]. Other repair enzymes, such as Escherichia coli Endonuclease VIII that excises oxidized pyrimidines from DNA, also contain a DNA-binding H2TH motif within the middle domain. The H2TH domains of these repair proteins are only peripherally involved in binding DNA; their primary function may be simply to position the N-terminal lobe and C-terminal zinc finger domain of the glycosylases for interactions with DNA.

The middle domain of topoisomerase IV-B subunit contains a H2TH motif that is structurally related to the DNA repair proteins. Although the H2TH domain appears to be retained in all archaeal and plant typeż IIB topoisomerases identified to date, it has no known function and has not been observed in other topoisomerase families [PubMed12505993].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 9 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a S13-like H2TH domain domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 9 hidden Markov models representing the S13-like H2TH domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]